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Internal motions and flexibility are essential for biological functions in proteins. To assess the internal fluctuations and conformational flexibility of proteins, reliable computational methods are needed. In this study, wavelet transformation was used to filter out the noise and facilitate investigating the internal positional fluctuations of enzymes within nuclear magnetic resonance (NMR) structure ensembles. Moreover, potential active sites were identified by combining with positional fluctuation score, sequence conservation, and solvent accessible surface area. Among the total 107 catalytic residues in 44 examined enzymes, 69 residues were identified correctly. Our results suggest that wavelet transform analysis of structure ensemble is applicable to extract essential fluctuation information of proteins; furthermore, analysis of positional fluctuations is helpful for the identification of catalytic residues. [ABSTRACT FROM AUTHOR]